These are the materials that we are presenting at the February 2017 GATK workshop in Leuven, Belgium.

Materials Link
DAY 1: GATK Best Practices talks
Slide decks presented on Day 1 Google Drive Folder
DAY 2: Germline variant discovery
Variant Discovery Tutorial Worksheet (Day 2 AM) PDF on Google Drive
Variant Filtering Tutorial Worksheet (Day 2 PM) PDF on Google Drive
Germline Data Bundle (Day 2) ZIP on Google Drive
DAY 3 AM: Somatic mutation discovery
MuTect2 Tutorial Worksheet (Day 3 AM) PDF on Google Drive
MuTect2 Data Bundle (Day 2) TAR.GZ on Google Drive
CNV Tutorial Worksheet (Day 3 AM) PDF on Google Drive
CNV Data Bundle (Day 3 AM) ZIP on GATK website
DAY 3 PM: Pipelining with WDL
WDL Pipelining Tutorial Worksheet (Day 3 PM) PDF on Google Drive
WDL Pipelining Data Bundle (Day 2) ZIP on Google Drive


ramiro2k on 19 Feb 2017


Hello, we teach a bioinformatics class at the University of Vermont, can we use some of your slides?

Geraldine_VdAuwera on 19 Feb 2017


@ramiro2k Sure, feel free to use anything you find useful, including the hands-on tutorial materials. We just ask that you provide an attribution notice and make students aware of this website and forum.

ramiro2k on 19 Feb 2017


Thank you!!

zejun on 19 Feb 2017


Hi, Where I can find the R/plotting.R script? Cheers Zejun

Sheila on 19 Feb 2017


@zejun Hi Zejun, You can find it in the Germline data bundle above. -Sheila

tschaefer on 19 Feb 2017


Great, thanks for sharing this!

Hannah66 on 19 Feb 2017


Hello, we would like to learn WDL at Upenn. Could we use some of your slides? We need your permission to see your slides on google driver. Many Thanks, Han-Jen Lin

Geraldine_VdAuwera on 19 Feb 2017


The access permissions to these files were restricted due to a technical error. Access will be restored shortly; apologies for the inconvenience.

Geraldine_VdAuwera on 19 Feb 2017


The files should be restored now; thank you for your patience. Let us know if you run into any more trouble.




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